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Method for judging gene type of fetus

A genotype and fetal technology, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problems of high cost, long cycle, and increased risk of miscarriage for pregnant women, and achieve the effect of cost saving and deep sequencing depth

Active Publication Date: 2014-12-03
SHANGHAI MAJORBIO BIO PHARM TECH
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Problems solved by technology

When detecting the genotype of the fetus, if the placental material is obtained through invasive experiments (such as amniocentesis) for genotyping, the risk of miscarriage for pregnant women will increase; if the haploid sequencing of the parents' genotypes is performed, the experiment is cumbersome The cycle is very long and costs a lot

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  • Method for judging gene type of fetus
  • Method for judging gene type of fetus
  • Method for judging gene type of fetus

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Experimental program
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Embodiment 1

[0048] The method for judging the fetal genotype of the present embodiment includes the following specific steps:

[0049] A. Extract the peripheral blood DNA samples of pregnant women, use exon capture amplification, and then use the existing next-generation gene sequencing technology to build a library for the samples and sequence them on the machine to obtain the original data.

[0050] B. Perform quality control on the original data, compare with the reference sequence, detect SNP, annotate and count.

[0051] C. Based on the four combinations of the genotypes of the pregnant woman and the fetus, the mixed Gaussian model of the minimum allele frequency of the SNP sites of the four combinations is calculated using the maximum expected value algorithm.

[0052]The four combinations are the first combination, the second combination, the third combination and the fourth combination. When both the pregnant woman and the fetus are homozygous, it is the first combination, and th...

Embodiment 2 to Embodiment 8

[0093] The remaining parts of Embodiment 2 to Embodiment 8 are the same as Embodiment 1, except that the original data of mother and daughter in a certain family downloaded from the Internet are different.

[0094] First download the raw data of mother (NA12892) and daughter (NA12878) in a family from the 1000 Genomes Project website.

[0095] The exon data of NA12892 (mother), the length of paired reads is 250bp, and the number is 30395088. The exon data of NA12878 (daughter), the length of paired reads is 76bp, and the number is 74057330.

[0096] Since the exon data of NA12892 (mother) is smaller than the exon data of NA12878 (daughter), the reads of the exon data of NA12878 (daughter) are randomly selected according to different ratios to form six new data, and then the GATK software is used to generate corresponding SNP files. Both the original data and the new data are mixed, and the mixing ratio is shown in Table 1.

[0097] Table 1 Example 2 to 7 data mixing table ...

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Abstract

The invention relates to a method for judging the gene type of a fetus. The method comprises the following specific steps: A, extracting a DNA (deoxyribonucleic acid) sample of peripheral blood of a pregnant woman, and carrying out exon sequencing to obtain original data; B, carrying out quality control on the original data, comparing with a reference sequence, detecting SNP (Single Nucleotide Polymorphism), annotating and counting; C, based on four combination modes of the gene types of the pregnant woman and the fetus, calculating to obtain the Gaussian mixture model of the minimum gene frequency of SNP sites with the four combination modes by using a maximum expected value algorithm; D, calculating to obtain three critical values of the Gaussian mixture model; E, judging the gene type of the fetus by comparing the minimum gene frequency of each SNP site with the three critical values. According to the method for judging the gene type of the fetus disclosed by the invention, the mutation site of fetal gene can be calculated by means of the peripheral blood of the pregnant woman, the method is accurate and safe, DNAs from the father do not need, the sequencing depth is deeper, the cost is reduced, and the method is economic and practical.

Description

technical field [0001] The invention relates to a method for inferring genotype based on a specific algorithm, which belongs to the field of biotechnology. Background technique [0002] Genotype, also known as hereditary type, is the general term for the combination of all genes of a certain organism. It reflects the genetic makeup of an organism, the sum of all genes acquired from both parents. It is estimated that there are about 50,000 pairs of structural genes in humans. Therefore, the genotype of the whole organism cannot be expressed, and the genotype used in genetics often refers to the genotype of a certain trait. In human chromosomes, the genetic traits are determined by the corresponding genes on a pair of chromosomes from the parents. Because the human body has two sets of chromosomes from the parents, it is also called diploid. [0003] The judgment result of genotype can be used as an intermediate result to provide data information for academic research, prev...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18
Inventor 陈昌岳王璇任一张祥林
Owner SHANGHAI MAJORBIO BIO PHARM TECH
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